Where to specify available dependencies?

[tischi]

Hi, each module needs dependencies to be running, typically a container. Is there a standard way how to link from the module to a file that explains how to build the container? I think this could be useful because if oneself or an agent wants to improve a module, it's good if they know what the dependencies are.

[krokicki]

There is a way to trace it, but I don't think it's documented anywhere.

For example, take this cellpose module:
https://github.com/BioImageTools/nextflow-modules/blob/main/modules/bits/cellpose/main.nf#L2

It uses the bioimagetools/cellpose:2.2.3-dask2023.10.1-py11 container, so you can pull that and get the labels:

docker pull ghcr.io/bioimagetools/cellpose:2.2.3-dask2023.10.1-py11
docker inspect ghcr.io/bioimagetools/cellpose:2.2.3-dask2023.10.1-py11 | jq '.[0].Config.Labels'

You'll see a standard OCI label that points to the repo that created it:

"org.opencontainers.image.source": "https://github.com/BioImageTools/containers",

And in that repo you can find the Dockerfile:
https://github.com/BioImageTools/containers/tree/main/cellpose/2.2.3-dask2023.10.1-py11

We do the labeling automatically in the build script:
https://github.com/BioImageTools/containers/blob/main/build.sh#L14